Provided a more general relation between resource count & disk space

set mtba image to latest

README.md

@@ -22,6 +22,7 @@ This repository is the starting point for any information and tools you will nee
     - [TLS terminating proxies](#tls-terminating-proxies)
     - [File structure](#file-structure)
     - [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
+    - [Loading data](#loading-data)
 4. [Things you should know](#things-you-should-know)
     - [Auto-Updates](#auto-updates)
     - [Auto-Backups](#auto-backups)
@@ -118,7 +119,7 @@ Mention:
 We will set the repository up for you. We will then send you:
 
 - A Repository Short Name (RSN). Beware: this is distinct from your site name.
-- Repository URL containing the acces token eg. https://BH_Dummy:dummy_token@git.verbis.dkfz.de/bbmri-bridgehead-configs/dummy.git
+- Repository URL containing the acces token eg. https://BH_Dummy:dummy_token@git.verbis.dkfz.de/<project>-bridgehead-configs/dummy.git
 
 During the installation, your Bridgehead will download your site's configuration from GitLab and you can review the details provided to us by email.
 
@@ -311,6 +312,32 @@ Once you edited the gitlab config, the bridgehead will autoupdate the config wit
 
 There will be a delay before the effects of Directory sync become visible. First, you will need to wait until the time you have specified in ```TIMER_CRON```. Second, the information will then be synchronized from your national node with the central European Directory. This can take up to 24 hours.
 
+### Loading data
+
+The data accessed by the federated search is held in the Bridgehead in a FHIR store (we use Blaze).
+
+You can load data into this store by using its FHIR API:
+
+```
+https://<Name of your server>/bbmri-localdatamanagement/fhir
+```
+The name of your server will generally be the full name of the VM that the Bridgehead runs on. You can alternatively supply an IP address.
+
+The FHIR API uses basic auth. You can find the credentials in `/etc/bridgehead/<project>.local.conf`.
+
+Note that if you don't have a DNS certificate for the Bridgehead, you will need to allow an insecure connection. E.g. with curl, use the `-k` flag.
+
+The storage space on your hard drive will depend on the number of FHIR resources that you intend to generate. This will be the sum of the number of patients/subjects, the number of samples, the number of conditions/diseases and the number of observations. As a general rule of thumb, you can assume that each resource will consume about 2 kilobytes of disk space.
+
+For more information on Blaze performance, please refer to [import performance](https://github.com/samply/blaze/blob/master/docs/performance/import.md).
+
+#### ETL for BBMRI and GBA
+
+Normally, you will need to build your own ETL to feed the Bridgehead. However, there is one case where a short cut might be available:
+- If you are using CentraXX as a BIMS and you have a FHIR-Export License, then you can employ standard mapping scripts that access the CentraXX-internal data structures and map the data onto the BBMRI FHIR profile. It may be necessary to adjust a few parameters, but this is nonetheless significantly easier than writing your own ETL.
+
+You can find the profiles for generating FHIR in [Simplifier](https://simplifier.net/bbmri.de/~resources?category=Profile).
+
 ## Things you should know
 
 ### Auto-Updates

ccp/docker-compose.yml

@@ -28,7 +28,7 @@ services:
       BLAZE_URL: "http://bridgehead-ccp-blaze:8080/fhir/"
       BEAM_PROXY_URL: http://beam-proxy:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      OBFUSCATE: "no"
+      EPSILON: 0.28
     depends_on:
       - "beam-proxy"
       - "blaze"

ccp/modules/mtba-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   mtba:
-    image: docker.verbis.dkfz.de/cache/samply/mtba:develop
+    image: docker.verbis.dkfz.de/cache/samply/mtba:latest
     container_name: bridgehead-mtba
     environment:
       BLAZE_STORE_URL: http://blaze:8080